Comparative Analysis of DNA and RNA Hydration Patterns:
Insights from Crystallographic Data

L. Biedermannová, B. Schneider

Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Prumyslova 595, 252 50 Vestec

Lada.Biedermannova@ibt.cas.cz


Understanding the hydration dynamics of nucleic acids is crucial for elucidating their structural stability and functional roles. Building upon our previous work on protein [1,2,3] and DNA hydration [4,5,6], we recently extended our analysis to include RNA, providing a comparative study of hydration patterns between the two nucleic acid types.

Expanding our dataset to encompass RNA crystal structures, we have conducted a detailed examination of hydration around selected conformational classes common for both DNA and RNA. By leveraging a multi-step approach, we analyzed hydration patterns around dinucleotide fragments extracted from a non-redundant set of high resolution crystallographic structures. Our dataset includes 2,727 DNA chains and now incorporates 206 RNA chains, allowing for a comprehensive investigation.

Utilizing Fourier averaging techniques, we computed water probability density distributions around dinucleotides, discerning hydration sites and revealing the nuanced interplay between water molecules and nucleic acid structure. By comparing hydration profiles between DNA and RNA, we aim to elucidate similarities and differences in their hydration landscapes.

This poster presentation will showcase our comparative analysis of DNA and RNA hydration, highlighting key findings and discussing the implications for understanding nucleic acid hydration dynamics. Our results offer valuable insights into the role of hydration in modulating nucleic acid structure and function.

Visitors to the poster can access our data and visualizations online at watlas.datmos.org/watna, facilitating further exploration and analysis of nucleic acid hydration patterns.

 

1. Biedermannová L. & Schneider B.: Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures. Acta Crystallographica D71, 2192-2202 (2015).

2. Černý J., Schneider B. & Biedermannová L.: WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations. Phys. Chem. Chem. Phys. 19, 17094 (2017).

3. Biedermannová L. & Schneider B.: Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. Biochimica et Biophysica Acta - General Subjects 1860, 1821-1835 (2016).

4. Schneider B. & Berman H.M.: Hydration of the DNA Bases Is Local. Biophysical J. 69, 2661-2669 (1995).

5. Schneider B., Patel K. & Berman H.M.: Hydration of the Phosphate Group in Double-Helical DNA. Biophysical J. 75, 2422-2434 (1998).

6. Biedermannová L., Černý, J., Malý, M., Nekardová, M., Schneider, B.: Prediction of DNA hydration from knowledge-based hydrated building blocks. Acta Cryst. D78, 1032-1045 (2022).L. Margilies, M. J. Kramer, R. W. McCallum, S. Kycia, D. R. Haeffner, J. C. Lang, A. I. Goldman, Rev .Sci. Instrum., 70, (1999), 3554.